The newspaper, citing confidential data that it obtained, said an investigation showed the NFL omitted more than 100 diagnosed concussions from studies the league commissioned from its teams and billed as comprehensive, including severe injuries to star quarterbacks Steve Young and Troy Aikman.

In a statement, the NFL said the Times exposé is “contradicted by clear facts that refute both the thesis of the story and each of its allegations.”

The Times said that when it asked the league about the missing cases – more than 10 percent of the total – officials acknowledged the teams were not required to submit their data and some did not. The NFL told the newspaper the missing cases were not an attempt to alter the rate of concussions and that should have been made clearer. Some of the “missing” concussions were found merely by cross-referencing the NFL teams’ own public injury reports.

Former and current NFL commissioners Roger Goodell and Paul TagliabueAP

“It should be an unmistakable red flag that a team does not report any concussions over multiple years,” Dr. Robert Cantu, a peer reviewer of the concussion committee’s analyses, told the Times. Multiple doctors who oversaw the league’s research declined to comment on their methods.

The NFL also objects to what it terms “pages of innuendo and speculation” outlining business connections between the league and the tobacco industry, which was engaged in a campaign to downplay the health risks of its product. The Times reported the two businesses shared lobbyists, lawyers and consultants, and Giants co-owner Preston R. Tisch was a prominent figure in the cigarette industry.

Earlier this month for the first time a top NFL official acknowledged a link between football-related concussions and chronic traumatic encephalopathy (CTE), the degenerative brain condition caused by repeated blows to the head.

A group of retired players sued the NFL accusing the league of covering up the risks of concussions. They won a settlement that could cost the league up to $1 billion but some players have appealed the settlement.

The league’s statement Thursday concluded: “The Times’ sensationalized story is further refuted by the NFL’s ongoing commitment on the issue of player health and safety – notably, to the support of research, including that of our most vocal critics, on the long-term effects of concussions in all sports, and to change our game in an effort to make the sport of football as safe as it can be.”